Ban the phrase “spatio-temporal”

Every time I read, hear or write the phrase “spatio-temporal” I cringe. It’s used frequently in developmental biology to convey the idea of measuring or studying something over both space and time. But it is an unusually awkward phrase, being an ugly sounding and looking hyphenation of a prefix “spatio” and adjective “temporal” that are rarely used on their own. There must be a better way to convey this concept. If not – we need to invent one. Ideas?

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R.I.P. Mark Fidrych

One of my all-time favorite baseball players – Mark “The Bird” Fidrych – died yesterday. He was one of the first baseball players I remember loving because of how he played, and not because he was on the Red Sox. The weird antics on the mound – he patted the dirt, and talked to the ball – were inspiring (I used to talk to the ball too, though it was a bit weirder since I was a catcher). 

I had a random brush with Fidrych in Boston after he retired (he was from Massachusetts, and after he flamed out with the Tigers, he made a brief comeback attempt with the PawSox). It was 1986, and my roommate Jason and I were at game 2 of the Sox-Angels ALCS (which the Sox won handily). We’d camped out outside Fenway for a couple of nights, and got great seats – 4th or 5th row right behind third base. And Fidrych was sitting a few rows in front of us (he was still instantly recognizable). Game went on – he was chatting with fans for a few innings. Then, somewhere around halfway through the game some guys in suits – late arrivals – showed up. And it turned out Fidrych was in their seats and the ushers sent him somewhere else. A perfect moment.

It happened that the Sox were in town yesterday to play the A’s, and a bunch of us went to the game. When I heard about Fidrych, I made a couple of signs – including one with Big Bird saying “R.I.P. Bird” (Fidrych famously appeared on the cover of Sports Illustrated with Big Bird). I held the signs up at the game, even though few people seemed to know who he was. And in the bottom of the 2nd inning, N.E.S.N. used it as the backdrop while Jerry Remy and Don Orsillo remembered Fidrych. Here’s the clip:

Recalling that ALCS encounter with Fidrych made me realize that I’ve actually had brief interactions with all three of my favorite players from my childhood: Fidrych, Sox pitcher Bill “Spaceman” Lee (who ran for President on the Rhinoceros Party ticket in 1988 and was campaigning among those of us camped out for Sox-A’s playoff tickets) and Dennis “Oil Can” Boyd (who once gave me a long explanation of how great a catcher he could have been while warming up for a game against Chicago in old Comiskey – I had a particular affection for The Can, because people used to call me “Oil Can” in elementary school, long before he reached the majors, for reasons I can not fathom, though they were definitely not being nice). 

R.I.P. Bird.

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[WARNING – BSG SPOILER] PopGen’s teachable moment – Hera, mtEve and the fate of the BSG survivors

I just finished watching the last episode of Battlestar Galactica. You could see for a while that it was going to turn out that we were all descendants of the survivors, but I’m embarrassed to say that I didn’t see the Hera – mitochondrial eve connection until the raptor swooped over the plains of east Africa.

After the episode ended, I started poking around to see what people are saying about the ending, and I was surprised at how often I came upon some version of the following exchange (from rc3.org):

There really is a Mitochondrial Eve — she is the earliest common ancestor all humans alive right now share. (I believe she lived about 90,000 years ago, so the 150,000 number on the show is wrong.)

What this implies is that none of the humans or cylons who wind up on Earth (other than Hera) are able to successfully reproduce, or that all of their progeny die out. Hera’s offspring are the only ones who make it. And indeed, none of the indigenous residents of Earth will have produced successful offspring, except through Hera.

Reader Rob then responded:

No, she’s the last common matrilineal ancestor of all living humans- all humans alive today have her mitochondrial DNA. She is NOT, however, the last common ancestor of all humans alive today… It should be remembered though that this does not mean that other women didn’t leave descendants whose are still alive. Mitochondrial-DNA is only inherited on the female side; a woman who had 10 male children but no females would be a mitochondrial dead end, but could have theoretically millions of descendants alive today.

This is hardly the only such exchange. Everywhere people are talking about BSG’s finale, they’re talking about population genetics. And they’re mostly getting it wrong. The “no other survivors have descendants” is the most common misconception, but others include: Hera being half-human, half-cylon means we all are; Hera had to have had at least one daughter (actually she would have had to have had at least two); the indigenous population must have died off; etc…

But on all the blogs and forums I’ve visited, people have corrected these misconceptions. It’s like there’s this big, organic lesson in human population genetics going on out there, as people collectively wrestle with the concept of mtEve, and – amazingly – generally converge on something approximating the right answer. I think it’s kind of cool.

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Nature: Big is beautiful

Nature has a brief “Research Highlight” on our recent PLoS One paper.

Nature 458, 263 (19 March 2009) | doi:10.1038/458263a; Published online 18 March 2009

Genomics: Big is beautiful

PLoS ONE 4, e4688 (2009)

Finding gene regulators in the fruitfly Drosophila melanogaster has proved difficult: looking for conserved non-coding DNA sequences, a method that works well in vertebrates, has been unsuccessful. Michael Eisen at the University of California, Berkeley, and his co-workers suggest that this is because the fly’s genome is compact — not because its regulatory architecture differs substantially from that of vertebrates.

Eisen’s group sequenced various loci from four species of tephritid — ‘true’ fruitflies — which have large genomes containing islands of conserved non-coding DNA sandwiched between unconserved stretches. This allowed the researchers to pinpoint six conserved tephritid non-coding regions that functioned as gene enhancers in D. melanogaster embryos. Until now, the compact size of the D. melanogaster genome has been considered a boon to scientists.

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NIH public access policy made “permanent”

The consolidated appropriations bill passed by Congress and signed into law on Wednesday has a provision that makes the NIH public access policy permanent:

[Via THOMAS] Sec. 217. The Director of the National Institutes of Health (`NIH’) shall require in the current fiscal year and thereafter that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine’s PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication, to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law.

I’ve highlighted the key phrase in red, which is the only difference between this year’s language and that of previous years. The effect of this language is that it will no longer be necessary for language enabling the public access policy to appear in the appropriations bill every year – it will just continue until Congress specifically ends it. Hence the idea that it is now “permanent”. 

Congrats and thanks to Heather Joseph at SPARC, Sharon Terry at the Genetics Alliance and the others who worked to make this happen.  

Of course, H.R. 801 still lurks, but I think it’s time to turn our attention to other things. In particular, having the policy apply to work funded by other government agencies (NSF in particular), and in working to make the 12 month delay shorter and shorter.

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PLoS and Drosophila Meeting T-shirts

A lot of people have asked about getting the various t-shirts I’ve made for PLoS and the Fly Meeting. I’ve posted the images for on zazzle.com if anyone wants a t-shirt of their own (proceeds go to PLoS).


create & buy custom products at Zazzle

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Why I hate bioethicists

Yuval Levin, former Executive Director of the President’s Council on Bioethics, has an op-ed in Tuesday’s Washington Post arguing that Obama’s new stem cell policy is dangerous. Levin does not argue that stem cell research is bad. Rather he is upset that Obama did not dictate which uses of stem cells are appropriate, but rather asked the National Institutes of Health to draft a policy on which uses of stem cells are appropriate: 

 

It [Obama’s policy] argues not for an ethical judgment regarding the moral worth of human embryos but, rather, that no ethical judgment is called for: that it is all a matter of science.

This is a dangerous misunderstanding. Science policy questions do often require a grasp of complex details, which scientists can help to clarify. But at their core they are questions of priorities and worldviews, just like other difficult policy judgments.

Lost in this superficially unobjectionable – if banal – assertion of the complexity of ethical issues involving science is Levin’s (and many other bioethicists) credo: that the moral complexity of scientific issues means that scientists should not make decisions about them.

This conflation of science and scientists is offensive and ignorant. In my experience, no one has thought about the moral side of scientific issues more deeply than scientists. While bioethicists like Levin prattle on, reminding us that there are difficult decisions to be made in science, scientists have to grapple constantly with the difficult moral dilemmas that arise from our research. 

Scientists are eager to make sure that the technologies we develop are used appropriately and deployed for the common good. And it is precisely the understanding of the subtle details of technology, and the creativity to see not only the obvious questions new technologies present, but the ones that may arises as the technology develops, that uniquely equip scientists to speak to their appropriate use.

This is not to say that all scientists would make the right moral decision – or that the public will necessarily agree with the scientific community on what is right. This is why whatever policy the NIH arrives at should and will be subject to public scrutiny. But it is important for the public to understand that the decision the NIH makes will surely be a moral one. 

Levin does not understand this. But fortunately Obama does. He decided to leave the decision on stem cell research to the NIH not because he felt that this was a technical decision, but rather because he trusts scientists to make the right moral decisions.

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Regulatin’ Genes

Via John Tierney, this video about development is awesome:

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Response to Conyers on Huff Po Front Page

I tightened up my earlier response to John Conyers’ letter, and it’s now on the Huffington Post front page. 

http://www.huffingtonpost.com/michael-eisen/john-conyers-tries-and-fa_b_172944.html

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John Conyers Tries [and Fails] to Explain His Position

Lawrence Lessig and I have been writing about the link between publisher contributions to members of the House Judiciary committee and their support for H.R. 801 – a bill that would end the newly implemented NIH public access policy that makes all works published as part of NIH funded research freely available to the public online. On Friday, House Judiciary chairman John Conyers (D-MI) – lead sponsor of the bill – responded in a letter on Huffington Post.

The first several paragraphs of Conyers’  letter contain an outline of his record as a progressive politician.  Representative Conyers is a smart man who has worked hard defending the public’s interest on a large number of issues. But no record, no matter how distinguished, can provide an excuse for introducing an atrocious piece of legislation that sacrifices the public interest to those of a select group of publishing companies who just happen – coincidentally I’m sure – to contribute to Representative Conyers and the other backers of the bill. 

Despite his protestations, Conyers response to our letter – like the bill itself – is taken straight from the playbook of the publishers who oppose the NIH public access policy, and only cements my opinion that he is doing this at their behest without taking the time to research or understand the issue. Although he says at several times he is trying to get to the bottom of a complex issue, he ignored evidence presented to his committee during hearings last year and has shown no interest in learning about how scientific publishing actually works. 

Conyers offers two main justifications for his support of H.R. 801. First, seems incensed that the bill mandating the policy originated in the Appropriations Committee and not his Judiciary Committee. Judiciary was the appropriate venue, he argues, because the bill alters copyright. As I will show below, this is incorrect. Second, Conyers trots out the publishers’ favorite trope that the NIH policy will bankrupt publishers and thereby destroy science. Since this is the more substantive claim, I will deal with it first. Here is what Conyers wrote:

… on the narrow merits of the issue, Professor Lessig and proponents of “open access” make a credible argument that requiring open publishing of government-funded research information furthers scientific inquiry. They speak out for important values and I respect their position.

While this approach appears to further and enhance access to scientific works, opponents argue that, in reality, it reverses a long-standing and highly successful copyright policy for federally-funded work and sets a precedent that will have significant negative consequences for scientific research.

These opponents argue that scientific journals expend their own, non-federal resources to manage the peer review process, where experts review academic publications. This process is critical because it provides the quality check against incorrect, reckless, and fraudulent science and furthers the overall quality and vigor of modern scientific debate. Journal publishers organize and pay for peer review with the proceeds they receive from the sale of subscriptions to their journals, thereby adding considerable value to the original manuscripts of research scientists.

The policy Professor Lessig supports, they argue, would limit publishers’ ability to charge for subscriptions since the same articles will soon be publicly available for free. If journals begin closing their doors or curtailing peer review, or foist peer review costs on academic authors (who are already pay from their limited budgets printing costs in some cases), the ultimate harm will be to open inquiry and scientific progress may be severe. And the journals most likely to be affected may be non-profit, scientific society based journals. Once again, a policy change slipped through the appropriations process in the dark of night may enhance open access to information, but it may have unintended consequences that are severe. 

This argument reflects several gross misconceptions about the nature of scientific publishing. The notion that the NIH policy will lead to massive subscription cancelations is not supported by empirical data or by publisher actions. 

The NIH policy require that works be available within 12 months of publication – not immediately. This delay of free public access was put in place precisely because it would allow publishers to recoup their investment in publishing by charging for access to the freshest material. Science moves far too fast for active researchers to afford a year’s delay before reading papers in their field. Thus universities and other research institutions have to maintain subscriptions to a wide range of journals. Many journals, realizing that their revenue comes primarily from new material, already make their contents freely available online after a year or less. And these journals have not reported a wave of canceled subscriptions – or any appreciable loss of revenue. 

Indeed, most publishers have no problem with the NIH policy. These include the most prestigious journals in biomedicine including NatureScience, the Proceedings of the National Academy of Sciences, the New England Journal of Medicine, as well as most other scientific societies, the publishing conglomerate Springer and, of course, true open access publishers like PLoS and BioMedCentral. Many even help their authors by sending copies of their articles directly to the NLM.  It is a small minority of narrow-minded and venal publishers who want this policy reversed. 

Second, publishers do not pay for peer review. Peer review is carried out by members of the research community, who receive no remuneration for this important contribution to the scientific process and the integrity of the scientific literature. Indeed, since the salaries of most American scientists are paid directly or indirectly by the US government, the peer review process can be viewed as a massive Federal subsidy to publishers. That some publishers – who not only get their most important source of skilled labor paid for by taxpayers but are also publishing research that is the product of tens of billions of annual taxpayer dollars – are unwilling to provide the taxpayers with a copy of the papers they paid to produce and review is unconscionable.

And while Representative Conyers’ publishing friends may have convinced him that there are severe unintended consequences that will arise from the NIH public access policy, the scientific community – who has been debating this issue for over a decade – strongly disagrees. Elias Zerhouni – who was NIH Director until last year – spent years crafting this policy in consultation with scientists, publishers, and members of Congress. It is strongly supported by his predecessor -Nobel laureate Harold Varmus – and a cadre of 32 of his American Nobel prizewinning colleagues. And the world’s leading private medical research organizations – the Howard Hughes Medical Institute and the Wellcome Trust – have, after extensive research and discussion, adopted even more aggressive policies than the NIH. Does Representative Conyers really think he better understands what’s good for science than they do all of these groups and people?

Now, let’s return to the issues of process and copyright, which seem to so infuriate Conyers:

… there is a serious process issue at stake here. My bill would restore longstanding federal copyright policy in this area. It reverses a provision slipped into an appropriations bill in the middle of the night, with no consultation with the Committee which is actually supposed to write the law in this area, the Judiciary Committee, which I chair. Thus, Professor Lessig simply ignores that this so-called “open access” policy was not subject to open hearings, open debate or open amendment in Congress and itself represents the sort of process-compromised special interest provision that he generally rails against. Now the special interests here may be highly worthy, but an openness hawk such as Professor Lessig ought not countenance procedural gimmicks just because they yielded a favored result.

My bill lays down a marker indicating that issues this complex, with important values and convincing arguments on both sides, should not be decided by a few lawmakers without relevant jurisdictional expertise in the dark of night with no meaningful public scrutiny or input. Unlike the measure my bill would repeal, my bill is fully available to the public and has my name attached to it. If it moves through my Committee, which it has not yet, it will be subject to full public hearings – and open to criticism and improvement from all sides.

As someone who has been involved with this issue and has closely followed the development of the NIH public access policy, I can say that Conyers’ history of this policy is grossly inaccurate. The NIH policy was developed over the course of several years, during which time there was extensive back and forth between Congress and the NIH as they worked to craft a policy that would ensure public access to taxpayer-funded research. 

I am no expert of Congressional protocol, but it seems perfectly sensible to me that the Appropriations Committee, whose job it is to make sure that taxpayers’ money is spent wisely and efficiently, would be the relevant committee for setting the terms under which scientists could receive federal dollars. Once developed, the policy was opened up to public comment. Everyone in the scientific research and publishing communities knew about the policy long before it was implemented, and then NIH Director Elias Zerhouni met with all stakeholders to make sure their views and issues were considered. This is hardly a bill snuck in by special interests and rammed through in the middle night with no public comment, as Conyers would have us believe. 

Conyers’ argument that the bill should have gone to his Judiciary committee rests on the dubious notion that NIH policy modifies copyright. But the policy in question does not alter copyright in any way. The NIH policy requires its grantees to make copies of their published papers available to the public. That’s it. This is a modification of the contract made between grantees and the NIH every time a new grant is awarded – a contract that already governs data release, publication, appropriate use of animals and other research subjects, etc…

Copyright only comes into the picture because some publishers force scientists, as a condition of publication, to sign away their right to make their papers available to the taxpayers who supported their research and salaries. NIH-funded scientists who still wish to publish in such journals have to amend these highly restrictive agreements so that they maintain the right to make a copy of their manuscript available to the public.

It is actually publication agreements like these that reverse longstanding tradition in scientific publication. Only recently have some journals – eager to exact more control over government funded research –  denied scientists their historical right to distribute manuscript copies of their papers to their colleagues and other interested parties.

When I started in science – before the internet became the primary means for disseminating research results – it was routine practice for my advisors to hand out copies of their papers to visitors and to mail manuscript versions of published papers to other scientists and members of the public – anyone who wrote to the lab asking for one. And almost since the internet was invented, scientists – especially physicists – took advantage of it to make the sharing of manuscripts more rapid and efficient. 

There is also a long tradition of providing free public access to print copies of papers describing taxpayer-funded research though the National Library of Medicine in Bethesda, MD, which is now simply continuing this tradition by making manuscript copies of papers available online. 

While publishers may find these traditions more irksome in the digital age, it is absurd for them to argue that scientists sharing papers with each other and the public is a radical new invention. 

The Copyright Act of 1976, which sets out most aspects of current copyright law, further undermines Conyers’ position that the NIH policy is incompatible with copyright. In Section 105 of the act Congress unambiguously recognizes the public right to have access to the product of federal research when they state that “Copyright protection under this title is not available for any work of the United States Government”. 

Although Congress left open the question of the copyright status of works funded by the US government, the drafters of the bill dealt clearly with this issue in the report language accompanying the bill:

A more difficult and far-reaching problem is whether the definition should be broadened to prohibit copyright in works prepared under U.S. Government contract or grant. As the bill is written, the Government agency concerned could determine in each case whether to allow an independent contractor or grantee to secure copyright in works prepared in whole or in part with the use of Government funds. The argument that has been made against allowing copyright in this situation is that the public should not be required to pay a “double subsidy,” and that it is inconsistent to prohibit copyright in works by Government employees while permitting private copyrights in a growing body of works created by persons who are paid with Government funds

Where, under the particular circumstances, Congress or the agency involved finds that the need to have a work freely available outweighs the need of the private author to secure copyright, the problem can be dealt with by specific legislation, agency regulations, or contractual restrictions.

So not only does the NIH policy not alter copyright, the NIH acted in precisely the way drafters of the Copyright Act said they should if they determined – as they have – that it would be beneficial to the public to have works funded by the NIH made freely available online. 

And even if we allow  – for the sake of argument only, because it is absurd –  Conyers his point, that this bill should have gone through Judiciary, is this really a valid excuse to overturn a good piece of public policy with a bad piece of legislation? 

Throughout his response Conyers repeatedly cites the need to discuss the complex issues around scientific publishing.  

I acknowledge that these are complex issues and that there are important values, strong arguments, and passionate supporters on both sides. And I look forward to the coming debate. 

Unfortunately, Representative Conyers actions do not reflect his words. This bill was introduced in the last Congress. The Judiciary Committee then held hearings on the bill, in which even the publishers’ own witnesses pointed out flaws in its logic and approach. In particular, a previous Registrar of Copyrights, clearly sympathetic to the publishers’ cause, acknowledged that the NIH Policy was in perfect accord with US copyright law and practice. If Conyers were so interested in dealing with a complex issue in a fair and reasonable way, why then did he completely ignore the results of this hearing and reintroduce the exact same bill – one that clearly reflects the opinions of only one side in this debate? 

Conyers concludes by saying:

I hope as the discussion moves forward, we can focus on the merits. 

I agree, and hope that when Representative Conyers finally begins to examine the merits of H.R. 801, he will realize that it should not move forward. 

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